Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
Fig 7
Depiction of two logic circuit regulatory pathways targeting PPIL2.
Two logic circuit regulatory pathways targeting the PPIL2 gene, an important cyclophilin member in immunological suppression, are found by Loregic: 1: PPIL2 is co-regulated by HDAC2 and SP1 forming the triplet of (RF1 is HDAC2, RF2 is SP1, T is PPIL2), which is consistent with the “T = ~RF1+RF2” gate (the ORN gate[22]), and SP1 is co-regulated by EGR1 and NFYA forming the triplet of (RF1 is EGR1, RF2 is NFYA, T is SP1), which is consistent with the “T = ~RF1*~RF2 (the NAND gate); 2: PPIL2 is also co-regulated by BRF1 and NFE2 forming the triplet of (RF1 is BRF1, RF2 is NFE2, T is PPIL2), which is consistent with OR gate, and NFE2 is co-regulated by TAL1 and GATA2 forming the triplet of (RF1 is TAL1, RF2 is GATA2, T is NFE2), which is also consistent with OR gate. We replace the triplets on these pathways using matched logic gates, and depict the pathways using logic circuits to summarize the regulatory logics targeting PPIL2 at the pathway level.